In 2005 Macintosh had to resign from his position as Deputy Convenor on the Standards Committee after it was revealed he had failed to declare £330 of hospitality from McDonald's within the required time.[9]

At the 2011 parliamentary election he once again defeated Jackson Carlaw with an increased majority of 2,012. The swing was 8.7% from Conservative to Labour.[15] Macintosh had feared losing the constituency following boundary changes[16] (with the removal of Barrhead, Neilston and Uplawmoor) which gave a notional Conservative majority of almost 3,500.[17] After the party's loss to the SNP, Macintosh was made Shadow Culture and External Affairs Secretary.[18] Only a week later, however, he took over the Shadow Education portfolio after MSP Malcolm Chisholm resigned over an internal party disagreement.[19]

At the 2016 election, Macintosh was pushed into third place behind Carlaw and the SNP's Stewart Maxwell. However, he was returned on Labour's regional list for West Scotland.[20]

On 28 October 2011, Macintosh officially launched his leadership campaign at Cumbernauld College in North Lanarkshire. He described the 2011 Holyrood election result as a "disaster", and that the party had been too negative[25] and if it did not change it "will consign ourselves to steady decline and years of opposition. We need to unite as a party and to start talking positively about our values, what Labour stands for and not just what we are against."[26]

In the ensuing leadership election, Macintosh came second to MSP Johann Lamont.

Despite lacking ministerial experience — "having never put a feather on the front bench"[27] — he was widely seen as a frontrunner in the leadership contest; however, UK Labour leader Ed Miliband was unable to recall Ken Macintosh's name during a TV interview with BBC Scotland, during the September 2011 Labour Party Conference.[28] After the interview, Miliband telephoned Macintosh to apologise for his mistake. Later, Macintosh tried to downplay the incident saying "I don't think anyone should read anything into it – half the time I can't even remember the names of my own kids."[29]

On 12 May 2016, Ken Macintosh was elected presiding officer with 71 votes on the third round of voting. He beat Murdo Fraser, Johann Lamont, John Scott and Elaine Smith. He suspended his Labour membership upon taking office, per the tradition that the Presiding Officer is strictly nonpartisan. In early November 2018 he created controversy when an MSP was sent out of Holyrood’s chamber for wearing a rainbow tie in support of LGBTI rights. Alex Cole-Hamilton, the Scottish Liberal Democrat, was told to change the garment by Macintosh because it flouted rules against “ostentatious campaign material”.